rs781487428
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_080704.4(TRPV1):c.1865G>C(p.Arg622Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 30)
Consequence
TRPV1
NM_080704.4 missense
NM_080704.4 missense
Scores
5
14
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.105
Genes affected
TRPV1 (HGNC:12716): (transient receptor potential cation channel subfamily V member 1) Capsaicin, the main pungent ingredient in hot chili peppers, elicits a sensation of burning pain by selectively activating sensory neurons that convey information about noxious stimuli to the central nervous system. The protein encoded by this gene is a receptor for capsaicin and is a non-selective cation channel that is structurally related to members of the TRP family of ion channels. This receptor is also activated by increases in temperature in the noxious range, suggesting that it functions as a transducer of painful thermal stimuli in vivo. Four transcript variants encoding the same protein, but with different 5' UTR sequence, have been described for this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.16475797).
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| TRPV1 | NM_080704.4 | c.1865G>C | p.Arg622Thr | missense_variant | Exon 14 of 17 | ENST00000572705.2 | NP_542435.2 | |
| TRPV1 | NM_018727.5 | c.1865G>C | p.Arg622Thr | missense_variant | Exon 13 of 16 | NP_061197.4 | ||
| TRPV1 | NM_080705.4 | c.1865G>C | p.Arg622Thr | missense_variant | Exon 13 of 16 | NP_542436.2 | ||
| TRPV1 | NM_080706.3 | c.1865G>C | p.Arg622Thr | missense_variant | Exon 12 of 15 | NP_542437.2 |
Ensembl
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
30
GnomAD3 exomes AF: 0.00000418 AC: 1AN: 239472Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 131118
GnomAD3 exomes
AF:
AC:
1
AN:
239472
Hom.:
AF XY:
AC XY:
0
AN XY:
131118
Gnomad AFR exome
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GnomAD4 exome Cov.: 33
GnomAD4 exome
Cov.:
33
GnomAD4 genome
GnomAD4 genome
Cov.:
30
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Uncertain
D
BayesDel_noAF
Uncertain
CADD
Benign
DANN
Benign
DEOGEN2
Uncertain
D;D;D;D;.;.;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
.;.;.;T;T;T;T
M_CAP
Uncertain
D
MetaRNN
Benign
T;T;T;T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;L;L;L;.;.;.
PrimateAI
Benign
T
PROVEAN
Benign
N;.;.;N;N;.;N
REVEL
Uncertain
Sift
Benign
T;.;.;T;T;.;T
Sift4G
Benign
T;T;T;T;T;T;T
Polyphen
B;B;B;B;B;.;B
Vest4
MutPred
0.34
.;.;.;.;Gain of loop (P = 0.0312);.;.;
MVP
MPC
0.092
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at